Splicing-dependent transcriptional gene silencing or activation

Abstract

Disclosed herein are methods for inhibiting or activating the transcription of a gene of interest, or inhibiting or activating the transcription of specific mRNA isoforms of a gene by using antisense oligonucleotides and/or small molecules. Also described herein are methods for activating transcription from a promoter and increasing overall gene expression by creating of a new splice site in a gene of a cell.

What is claimed is: 
     
       1. A method comprising inhibiting or activating transcription in a gene of a cell by:
 identifying a gene having an exon-mediated activation of transcription starts (EMATS) structure, wherein the EMATS structure comprises a weak transcription start site within 5 kb upstream of a highly included alternative internal exon, wherein the weak transcription start site has an average activity that is less than a median activity of a human transcription start site, and wherein the highly included internal exon comprises an exon flanked by introns whose average inclusion level, measured as percent spliced in (PSI), is greater than a median PSI of alternative internal exons; 
 selecting an antisense oligonucleotide or small molecule that is targeted to the highly included alternative internal exon; and 
 contacting the cell with the antisense oligonucleotide or small molecule to inhibit transcription from the weak transcription start site or to activate transcription from the weak transcription start site. 
 
     
     
       2. The method of  claim 1 , wherein the antisense oligonucleotide (ASO) is a morpholino oligonucleotide, a phosphorothioate ASO, a 2′-O-methyl (2′-OMe) ASO, 2′-O-methoxyethyl (2′MOE) ASO, a locked nucleic acid (LNA) ASO, a peptide-conjugated phosphorodiamidate morpholino (PMO) ASO or a Vivo-linked phosphorodiamidate morpholino (VPMO). 
     
     
       3. The method of  claim 1 , wherein the antisense oligonucleotide or small molecule is targeted for the 3′ splice site or 5′ splice site of the internal exon. 
     
     
       4. The method of  claim 1 , wherein transcription from the weak transcription start site is inhibited and the gene is HTT, NOTCH2 gene, MEN1 gene, dystrophin gene or p53 gene. 
     
     
       5. The method of  claim 1 , wherein the gene is associated with myotonic dystrophy type I or with Huntington's disease. 
     
     
       6. The method of  claim 1 , wherein the gene is an oncogene or an antioncogene. 
     
     
       7. The method of  claim 6 , wherein the oncogene is c-myc, Ras, STAT3, or bcl-2. 
     
     
       8. The method of  claim 1 , wherein the antisense oligonucleotide- or small molecule is targeted to an intronic silencing element. 
     
     
       9. The method of  claim 1 , wherein the gene encodes a therapeutic protein. 
     
     
       10. The method of  claim 9 , wherein the therapeutic protein is p53, pRb, PTEN, pVHL, APC, BRCA1, BRCA2, CD95, ST5, YPEL3, ST7, or ST14. 
     
     
       11. The method of  claim 1 , wherein the antisense oligonucleotide is a splice switching oligonucleotide. 
     
     
       12. The method of  claim 1 , wherein transcription from the weak transcription start site/promoter is activated and the gene is MLH3 gene, dystrophin gene or utrophin gene. 
     
     
       13. The method of  claim 1 , wherein the antisense oligonucleotide- or small molecule is targeted to a silencing element that is downstream or upstream of a skipped exon. 
     
     
       14. The method of  claim 1 , wherein the antisense oligonucleotide- or small molecule is targeted to an exonic silencing element on a skipped exon.